atacPairedEnd: pull in (filter and assemble as an object) some or all of the...

Description Usage Arguments Value Examples

View source: R/atacPairedEnd.R

Description

pull in (filter and assemble as an object) some or all of the "useful" reads in a paired-end ATACseq run (i.e., the majority of ATACseq studies)

Usage

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atacPairedEnd(bam, genome = c("hg19", "mm10"), bamParams = NULL,
  which = NULL, ...)

Arguments

bam

character string, the BAM file to parse

genome

optional character string, the genome assembly to target

bamParams

optional any parameters to pass through to ScanBamParam

which

optional a GRanges object with specific regions to extract

Value

a GenomicAlignmentPairs object

Examples

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## Not run: 

data(cytobands_hg19)
del7q <- byBand(cytobands_hg19)$chr7q22.1
galp <- atacPairedEnd('chr7.q10.CD49f_r1.hg19.bam', which=del7q)

library(Mus.musculus)
SMO <- transcriptsBy(Mus.musculus, 'gene')[['319757']]
galp <- atacPairedEnd('A1.SMO.bam', which=SMO)

library(Mus.musculus)
chr6 <- GRanges('chr6', IRanges(1, seqlengths(Mus.musculus)['chr6']), '*')
galp <- atacPairedEnd("A2.mm10.unique.bam",
                      bamParams=properPairedEndAtacFilters(which=chr6))

## End(Not run)

biobenkj/ATACseeker documentation built on Oct. 8, 2018, 11:11 a.m.